Yes, there are differences between the counter and sit-down services at these restaurants. Think of the counter service area as more of a fast-food option. I have noticed the prices are a little cheaper for the counter service, and the menus are more expansive for the sit-downs. The only restaurant where we have had the experience of both the sit-down and counter service is Jazz Kitchen (and Jazz Kitchen Express). We liked the food at both places, but the food at the Express was more fast-food like, and the food inside the restaurant tasted higher quality.
We have generally eaten at DtD restaurants without priority seatings. We have almost always had some wait though even eating at off-peak times. If you want to eat at a peak time of day or busy time of year and don't want to wait for an extended time, you would do best to make a priority seating.
